.hack//G.U. takes place in an alternate version of Earth in the year 2017. As depicted in the first .hack game series, the "2nd Network Crisis" was an incident that occurred seven years ago in which many computer systems across Japan malfunctioned. Through the efforts of those games' hero, Kite, the incident resulted in the birth of Aura, the ultimate artificial intelligence (AI), capable of making decisions for itself. Under the guidance of Aura, The World, the most popular massively multiplayer online role-playing game at the time, flourishes and the events of .hack//Legend of the Twilight occur during this four-year period.

In late 2014, Aura disappears, resulting in the slow decay of The World and the Internet as a whole. In response, the company that administrates The World, CC Corp, sets up "Project G.U." and tasks them with remedying the problem. They come up with the "Restore Aura (RA) Plan", in which they attempt to retrieve the fragments of Morganna--an AI that served as Aura's "mother"--and seal them into player characters (PCs) of The World. In theory, this would allow the Project G.U. programmers to manipulate the Morganna program to recreate Aura. Only certain "chosen" players could control these special "Epitaph PCs".

After locating candidates to operate the Epitaph PCs, the team proceeds to test the RA Plan despite concerns over "anti-existences" that might damage the Internet. The program fails catastrophically and destroys over 80% of the data for The World. Instead of trying to salvage the data, CC Corp develops The World R:2 and releases it to a new generation of players. However, this new game is less popular than its predecessor and becomes plagued by "player killers" (PKs), players who target other players for fun and sport. The Epitaph PCs which had been lost during the RA Plan disaster resurface in the new version, attached to certain players of interest.

.hack//G.U. simulates a massively multiplayer online role-playing game; players assume the role of a participant in a fictional game called The World. While in The World, the player controls the on-screen player character, Haseo, from a third-person person perspective (with optional first-person mode). Within the fictional game, players explore monster-infested fields and dungeons as well as "Root Towns" that are free of combat. They also can "log-off" from the game and return to a computer desktop interface which includes in-game e-mail, news, and message boards, as well as desktop and background music customization options. In Reminisce, an optional card game called "Crimson VS" becomes available.